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- PDB-9i5h: Structure of the bacterial archaellum from L. aerophila -

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Basic information

Entry
Database: PDB / ID: 9i5h
TitleStructure of the bacterial archaellum from L. aerophila
ComponentsFlagellin
KeywordsPROTEIN FIBRIL / Helical / cell surface structure / motility / archaellum
Function / homologyFlagellin, archaea / Archaebacterial flagellin / Flagellin/pilin, N-terminal / archaeal or bacterial-type flagellum-dependent cell motility / structural molecule activity / membrane / Flagellin
Function and homology information
Biological speciesLitorilinea aerophila (bacteria)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 2.7 Å
AuthorsSivabalasarma, S. / Taib, N. / Mollat, C.L. / Joest, M. / Steimle, S. / Gribaldo, S. / Albers, S.-V.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)403222702 Germany
CitationJournal: Biorxiv / Year: 2025
Title: Horizontal gene transfer of the functional archaellum machinery to Bacteria
Authors: Sivabalasarma, S. / Taib, N. / Mollat, C.L. / Joest, M. / Steimle, S. / Gribaldo, S. / Albers, S.V.
History
DepositionJan 28, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 21, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: Flagellin
D: Flagellin
E: Flagellin
F: Flagellin
G: Flagellin
H: Flagellin
I: Flagellin
J: Flagellin
K: Flagellin
L: Flagellin
M: Flagellin
N: Flagellin
O: Flagellin
P: Flagellin
Q: Flagellin
R: Flagellin
S: Flagellin


Theoretical massNumber of molelcules
Total (without water)330,96717
Polymers330,96717
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein
Flagellin


Mass: 19468.656 Da / Num. of mol.: 17 / Source method: isolated from a natural source / Source: (natural) Litorilinea aerophila (bacteria) / Strain: DSM:25763 / References: UniProt: A0A540VDN8
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: FILAMENT / 3D reconstruction method: helical reconstruction

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Sample preparation

ComponentName: Archaellum filament of L. aerophila / Type: ORGANELLE OR CELLULAR COMPONENT
Details: Archaellum filament isolated from the cell surface of L. aerophila
Entity ID: all / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Litorilinea aerophila (bacteria) / Strain: DSM:25763 / Cellular location: cell surface
Buffer solutionpH: 7.4 / Details: 2% NaCl in 1x PBS, pH 7.4
Buffer component
IDConc.NameFormulaBuffer-ID
12 %sodium chlorideNaCl1
21 xphosphate buffered salinePBS1
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: sheared and purified archaella filament from L. aerophila
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/2
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 295.15 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Calibrated magnification: 130000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 500 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 40 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)
EM imaging opticsEnergyfilter name: TFS Selectris / Energyfilter slit width: 10 eV

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Processing

EM software
IDNameVersionCategory
2EPU3.6image acquisition
12cryoSPARCv4.63D reconstruction
13PHENIX1.18.2_3874model refinement
CTF correctionType: NONE
Helical symmertyAngular rotation/subunit: 108.14 ° / Axial rise/subunit: 5.64 Å / Axial symmetry: C1
3D reconstructionResolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 1610077 / Num. of class averages: 20 / Symmetry type: HELICAL
RefinementStereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00723673
ELECTRON MICROSCOPYf_angle_d0.60832459
ELECTRON MICROSCOPYf_dihedral_angle_d16.8843263
ELECTRON MICROSCOPYf_chiral_restr0.054163
ELECTRON MICROSCOPYf_plane_restr0.0034130

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